LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-584-g3e8807bee0-modified)
  using 1 OpenMP thread(s) per MPI task
# 250 toluene system for drude polarizability example (Langevin)

units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style fourier
special_bonds lj/coul 0.0 0.0 0.5

pair_style lj/cut/thole/long 2.600 8.0 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4

read_data data.toluene extra/special/per/atom 1
Reading data file ...
  orthogonal box = (-18.290765 -18.163588 -18.223046) to (18.335673 18.162094 18.328654)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  5500 atoms
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  8 = max dihedrals/atom
  scanning impropers ...
  2 = max impropers/atom
  orthogonal box = (-18.290765 -18.163588 -18.223046) to (18.335673 18.162094 18.328654)
  1 by 1 by 1 MPI processor grid
  reading bonds ...
  5500 bonds
  reading angles ...
  6000 angles
  reading dihedrals ...
  6000 dihedrals
  reading impropers ...
  1500 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0.5     
  special bond factors coul:  0        0        0.5     
     5 = max # of 1-2 neighbors
    10 = max # of 1-3 neighbors
    16 = max # of 1-4 neighbors
    20 = max # of special neighbors
  special bonds CPU = 0.002 seconds
  read_data CPU = 0.039 seconds

comm_modify vel yes

group gTOLUENE molecule 1:250
5500 atoms in group gTOLUENE
group gCORES type 1 2 3 4 5 6 7
3750 atoms in group gCORES
group gDRUDES type 8 9 10 11 12
1750 atoms in group gDRUDES

pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT

neighbor 2.0 bin

variable vTEMP   equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS  equal 1.0

velocity gCORES  create ${vTEMP} 12345
velocity gCORES  create 260 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345

fix fDRUDE all drude C C C C C N N D D D D D

fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
Finding SHAKE clusters ...
    1250 = # of size 2 clusters
       0 = # of size 3 clusters
     250 = # of size 4 clusters
       0 = # of frozen angles
  find clusters CPU = 0.000 seconds

fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
fix fNPH all nve

compute cTEMP all temp/drude

thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50

timestep 0.5
run 2000
PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.38201098
  grid = 40 40 40
  stencil order = 5
  estimated absolute RMS force accuracy = 0.032593379
  estimated relative force accuracy = 9.8153994e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 103823 64000
Generated 10 of 66 mixed pair_coeff terms from geometric mixing rule
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 19
New max number of 1-2 to 1-4 neighbors: 20 (+1)
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10
  ghost atom cutoff = 10
  binsize = 5, bins = 8 8 8
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut/thole/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 42.31 | 42.31 | 42.31 Mbytes
   Step         TotEng         KinEng          Temp          PotEng         E_bond        E_angle        E_dihed        E_impro         E_vdwl         E_coul         E_long         Press          Volume       c_cTEMP[1]     c_cTEMP[2]  
         0   11086.38       2910.7282      202.07402      8175.6516      6565.4851      20.333365      1.0706727e-06 -3299.85        4972.8631      1306116.7     -1306199.8      40273.655      48631.318      314.89553      3.1777821    
        50   4782.1728      4728.7424      328.28759      53.430438      1812.2218      685.37821      683.70916     -3277.1645      797.34329      1305983.2     -1306631.2      16874.338      48631.318      448.52417      116.2546     
       100   2906.0897      3699.8048      256.85476     -793.71504      978.14865      778.36904      862.30899     -3270.1722      468.44899      1306096.8     -1306707.6      15631.404      48631.318      382.26409      35.748694    
       150   2089.0957      3593.049       249.44337     -1503.9533      751.32936      803.47809      668.47567     -3277.5983      128.17461      1306138.5     -1306716.3      15193.048      48631.318      384.75627      10.892371    
       200   1547.3333      3248.6384      225.53305     -1701.3051      699.66896      814.3117       692.83224     -3276.3957     -66.671737      1306160.9     -1306725.9      13787.659      48631.318      351.28239      3.8457998    
       250   1177.9348      3095.9487      214.93274     -1918.0139      688.88197      842.44523      615.89221     -3278.4465     -210.06161      1306154.3     -1306731        8808.5657      48631.318      335.81148      1.8330842    
       300   895.90519      2870.345       199.27046     -1974.4399      734.96369      858.58152      624.00856     -3278.6022     -342.01938      1306163.6     -1306735        3388.4792      48631.318      311.56813      1.2987947    
       350   669.25895      2764.9588      191.95414     -2095.6998      662.4477       860.797        602.69561     -3278.776      -376.37058      1306172.3     -1306738.8      8494.9167      48631.318      300.19413      1.13588      
       400   531.21827      2722.6772      189.01879     -2191.459       684.34789      868.77817      576.86094     -3280.1649     -459.666        1306160       -1306741.6      6726.2946      48631.318      295.59618      1.1315655    
       450   427.05596      2611.759       181.31841     -2184.703       719.21122      891.88163      591.22817     -3279.339      -534.65062      1306172.2     -1306745.2      2398.5235      48631.318      283.56127      1.0726276    
       500   310.44917      2556.0965      177.45411     -2245.6473      720.87336      841.50182      586.34159     -3279.3029     -539.81707      1306169.5     -1306744.8      3028.5931      48631.318      277.52311      1.0406455    
       550   207.83463      2531.3049      175.73298     -2323.4702      674.72039      855.21306      555.53214     -3280.0378     -553.93199      1306171.9     -1306746.9      4609.4426      48631.318      274.80627      1.0748604    
       600   88.814546      2459.9055      170.77616     -2371.0909      692.45642      834.47494      550.85907     -3280.9086     -595.31799      1306171.4     -1306744        2107.9852      48631.318      267.06307      1.0301874    
       650   75.618171      2416.9743      167.79571     -2341.3561      703.57678      869.98941      564.81202     -3280.7522     -619.80151      1306168       -1306747.2      1236.4721      48631.318      262.35416      1.0968323    
       700   49.83102       2415.7342      167.70961     -2365.9031      683.62354      882.67905      555.2357      -3280.7778     -615.06833      1306159.8     -1306751.4      2985.7098      48631.318      262.23092      1.0762415    
       750   41.512006      2427.2176      168.50684     -2385.7056      698.88264      863.2939       564.58201     -3280.0156     -637.29944      1306160.1     -1306755.3      1653.1221      48631.318      263.49799      1.0451917    
       800   109.5319       2481.904       172.30338     -2372.3721      697.23378      897.36558      561.28731     -3280.6784     -651.29556      1306155       -1306751.3      1219.8659      48631.318      269.43697      1.0647916    
       850   98.142967      2502.3128      173.72024     -2404.1698      696.54463      878.83288      566.44311     -3280.2837     -663.9458       1306155.6     -1306757.4      1122.7393      48631.318      271.67712      1.0302724    
       900   62.993993      2409.7323      167.29294     -2346.7383      722.01163      896.64655      560.66075     -3279.4915     -644.0544       1306153.6     -1306756.1      1604.2972      48631.318      261.58654      1.0609922    
       950   5.6725516      2403.5066      166.86073     -2397.8341      725.07855      891.00225      556.81975     -3279.7848     -672.66387      1306141       -1306759.2      1019.2026      48631.318      260.91186      1.0562452    
      1000   38.528474      2444.9706      169.73932     -2406.4421      704.73545      920.68469      534.59019     -3281.2673     -667.78073      1306141.1     -1306758.5      486.79189      48631.318      265.39933      1.0984922    
      1050   21.695785      2388.6306      165.82797     -2366.9348      712.16114      934.39222      546.92031     -3281.1469     -654.74447      1306137.4     -1306761.9      1556.0972      48631.318      259.28202      1.0760965    
      1100  -26.971861      2433.8425      168.96676     -2460.8144      710.1186       881.19203      524.51552     -3281.7925     -667.53168      1306137.1     -1306764.4      1203.8981      48631.318      264.20437      1.0706115    
      1150  -49.177478      2375.9684      164.94892     -2425.1459      729.78675      918.79571      518.21986     -3281.6542     -675.72373      1306130.4     -1306765        229.40771      48631.318      257.89841      1.0865156    
      1200  -53.424499      2422.0088      168.14522     -2475.4333      710.67987      884.25869      523.32531     -3282.2275     -674.49348      1306130.9     -1306767.9     -131.10564      48631.318      262.91122      1.0804683    
      1250  -58.534875      2394.4033      166.22874     -2452.9381      680.28126      909.58082      532.8195      -3281.5551     -653.13697      1306127       -1306767.9      546.9364       48631.318      259.92917      1.0425105    
      1300  -24.149411      2431.9907      168.83821     -2456.1402      681.27658      919.39227      536.41908     -3281.3717     -661.90882      1306121.5     -1306771.5      1455.7455      48631.318      264.00718      1.0630584    
      1350  -38.969674      2438.6198      169.29842     -2477.5894      707.96752      912.62534      519.44532     -3281.6739     -687.67146      1306126.1     -1306774.4     -1470.4402      48631.318      264.70227      1.1091837    
      1400   11.89647       2384.5408      165.54405     -2372.6443      719.04144      950.93215      550.56382     -3280.4581     -663.4919       1306122       -1306771.3      465.12463      48631.318      258.83564      1.0785513    
      1450  -13.1161        2436.6244      169.15989     -2449.7405      661.0505       933.0711       561.29529     -3280.6997     -672.68485      1306123.9     -1306775.7     -108.46561      48631.318      264.50632      1.0719062    
      1500  -38.153652      2417.4852      167.83118     -2455.6389      688.82141      892.35641      565.29001     -3279.6716     -662.18178      1306116.9     -1306777.2      517.90124      48631.318      262.44552      1.0338097    
      1550  -71.665266      2405.7012      167.01309     -2477.3665      681.7961       876.31285      559.00263     -3280.451      -649.16658      1306112.8     -1306777.7      925.48096      48631.318      261.14795      1.0609826    
      1600  -13.899093      2419.4802      167.96968     -2433.3793      718.47103      909.67972      559.06785     -3280.8163     -667.60798      1306108       -1306780.2      13.956417      48631.318      262.63622      1.0802668    
      1650  -16.406038      2431.0762      168.77472     -2447.4823      711.00182      907.65673      551.60307     -3279.8852     -661.525        1306104.4     -1306780.8      726.89849      48631.318      263.91566      1.0489975    
      1700  -18.55642       2438.2061      169.2697      -2456.7625      665.91204      943.02176      542.86545     -3280.9017     -657.99068      1306108       -1306777.7      801.43786      48631.318      264.67661      1.0750762    
      1750  -6.9247576      2443.9693      169.6698      -2450.894       733.24174      890.06829      560.83207     -3280.362      -670.93864      1306098.3     -1306782.1      47.132281      48631.318      265.30876      1.0661166    
      1800  -21.682431      2434.3385      169.0012      -2456.0209      729.35871      899.97223      561.5964      -3280.4727     -680.98586      1306096.5     -1306782        495.61385      48631.318      264.25734      1.0723673    
      1850  -72.914651      2408.8258      167.23001     -2481.7405      683.25604      904.13379      549.97668     -3279.6699     -652.62977      1306099.2     -1306786       -120.65343      48631.318      261.48508      1.0659867    
      1900  -55.402475      2415.4548      167.69022     -2470.8573      700.45259      904.7273       565.5276      -3280.4533     -673.2291       1306099.6     -1306787.4      202.17091      48631.318      262.2035       1.070996     
      1950  -79.873113      2409.2409      167.25883     -2489.114       695.95974      894.45123      564.70279     -3279.3581     -680.33608      1306100.8     -1306785.3      213.65765      48631.318      261.53032      1.0658627    
      2000  -102.20547      2399.4255      166.5774      -2501.631       689.68722      894.58548      565.53465     -3280.7594     -680.39656      1306096.4     -1306786.6      1113.6956      48631.318      260.46301      1.0647152    
Loop time of 38.7392 on 1 procs for 2000 steps with 5500 atoms

Performance: 2.230 ns/day, 10.761 hours/ns, 51.627 timesteps/s, 283.950 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 27.188     | 27.188     | 27.188     |   0.0 | 70.18
Bond    | 1.8867     | 1.8867     | 1.8867     |   0.0 |  4.87
Kspace  | 7.91       | 7.91       | 7.91       |   0.0 | 20.42
Neigh   | 0.71328    | 0.71328    | 0.71328    |   0.0 |  1.84
Comm    | 0.16597    | 0.16597    | 0.16597    |   0.0 |  0.43
Output  | 0.0024948  | 0.0024948  | 0.0024948  |   0.0 |  0.01
Modify  | 0.84082    | 0.84082    | 0.84082    |   0.0 |  2.17
Other   |            | 0.03234    |            |       |  0.08

Nlocal:           5500 ave        5500 max        5500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          13157 ave       13157 max       13157 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    1.33822e+06 ave 1.33822e+06 max 1.33822e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1338215
Ave neighs/atom = 243.31182
Ave special neighs/atom = 15.636364
Neighbor list builds = 32
Dangerous builds = 0
Total wall time: 0:00:38
